UniProt to patent data

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Posts: 1
Joined: Thu Jul 18, 2019 9:27 am

UniProt to patent data

Post by jerven » Thu Jul 18, 2019 9:43 am

Dear EPO,

It is now possible to do searches from UniProt to the EPO linked data sparql endpoint.
UniProt is a large data base in the life sciences with a professionally supported sparql endpoint and
RDF production that has been running for 15 years.

The combination of UniProt and EPO allow us to answer questions like which proteins where described in
patent publications for which the patent was granted more than 20 years ago. Try this example at https://sparql.uniprot.org

Code: Select all

PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
PREFIX skos:<http://www.w3.org/2004/02/skos/core#> 
PREFIX up:<http://purl.uniprot.org/core/> 
prefix patent: <http://data.epo.org/linked-data/def/patent/>
SELECT ?grantDate ?patent ?application ?applicationNo
  ?citation a up:Patent_Citation ;
  skos:exactMatch ?patent .
  BIND(SUBSTR(STR(?patent), 35) AS ?applicationNo)
  BIND(SUBSTR(STR(?patent), 33, 2) AS ?countryCode)
    ?publication patent:publicationNumber ?applicationNo ;
                 patent:application ?application . 
    ?application patent:grantDate ?grantDate .
  BIND((year(now()) - 20) AS ?thisYearMinusTwenty)
  BIND(year(?grantDate) AS ?grantYear)
  FILTER(?grantYear < ?thisYearMinusTwenty)
} ORDER BY ?grantYear
Now you notice that there are quite a few modelling differences. Some of which can be improved.

For example

Code: Select all

citation:SIP70B9B735F3162330 rdf:type up:Patent_Citation ;
  up:title "DNA sequences coding for the DR beta-chain locus of the human lymphocyte antigen complex and polypeptides, diagnostic typing processes and products related thereto." ;
  up:author "Mach B.F." ,
    "Long E.O." ,
    "Wake C.T." ;
  up:date "1984-03-28"^^xsd:date ;
  skos:exactMatch <http://purl.uniprot.org/patents/EP0103960> .
Is actually matching https://data.epo.org/linked-data/data/p ... 03960/A2/-

I was wondering how we can better allign the UniProt citations model with the EPO one.
And if the query I posted above is misleading in some way. Considering my limited knowledge of the EPO data model.


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